[Bioperl-l] Module to draw transmembrane protein topology

Tim Nugent t.nugent at cs.ucl.ac.uk
Tue Feb 20 10:50:10 EST 2007

Labeling of inside/outside and membrane is already possible via 
-inside_label, -outside_label and -membrane_label tags, defaults are 
intracellular, extracellular and plasma membrane.

Was definitely going to add an input/parser for MEMSAT, developed here 
at UCL, and probably a few other popular TM predictors too, e.g. 
PHOBIUS, TMHMM etc. Can already accept topology in the string format 
used by OPM (http://opm.phar.umich.edu/).


Chris Fields wrote:
> Sorry, I sent that last one off prematurely.
> I could see this being used as a very useful utility if a Bioperl object 
> had SeqFeatures which described transmembrane regions, or if output from 
> something like TMHMM were parsed and used for input.  Don't know if it's 
> included, but if not you probably should allow labeling of the 
> intracellular/extracellular space to designate periplasmic space, 
> mitochondrial matrix, thylakoid, etc.
> I think Bio::Graphics namespace is definitely the place to go.  If I 
> ever get around to writing up the RNA structural stuff I may put 
> something there myself.
> chris
> On Feb 20, 2007, at 8:31 AM, Tim Nugent wrote:
>> Thanks Chris, glad it's appreciated.
>> Is there anything else I can do? If anyone has any requests/suggestions
>> please let me know too.
>> Best wishes,
>> Tim

Tim Nugent (MRes)
Research Student
Bioinformatics Unit
Department of Computer Science
University College London
Gower Street
London WC1E 6BT
Tel: 020-7679-0410
t.nugent at ucl.ac.uk

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